Gonul Filoglu

52 additional reference population samples for the 55 AISNP panel

Ancestry inference for a person using a panel of SNPs depends on the variation of frequencies of those SNPs around the world and the amount of reference data available for calculation/comparison. The Kidd Lab panel of 55 AISNPs has been incorporated in commercial kits by both Life Technologies and Illumina for massively parallel sequencing. Therefore, a larger set of reference populations will be useful for researchers using those kits. We have added reference population allele frequencies for 52 population samples to the 73 previously entered so that there are now allele frequencies publicly available in ALFRED and FROG-kb for a total of 125 population samples.

Inference of biogeographical ancestry across central regions of Eurasia

The inference of biogeographical ancestry (BGA) can provide useful information for forensic investigators when there are no suspects to be compared with DNA collected at the crime scene or when no DNA database matches exist. Although public databases are increasing in size and population scope, there is a lack of information regarding genetic variation in Eurasian populations, especially in central regions such as the Middle East. Inhabitants of these regions show a high degree of genetic admixture, characterized by an allele frequency cline running from NW Europe to East Asia. Although a proper differentiation has been established between the cline extremes of western Europe and South Asia, populations geographically located in between, i.e, Middle East and Mediterranean populations, require more detailed study in order to characterize their genetic background as well as to further understand their demographic histories. To initiate these studies, three ancestry informative SNP (AI-SNP) multiplex panels: the SNPforID 34-plex, Eurasiaplex and a novel 33-plex assay were used to describe the ancestry patterns of a total of 24 populations ranging across the longitudinal axis from NW Europe to East Asia. Different ancestry inference approaches, including STRUCTURE, PCA, DAPC and Snipper Bayes analysis, were applied to determine relationships among populations. The structure results show differentiation between continental groups and a NW to SE allele frequency cline running across Eurasian populations. This study adds useful population data that could be used as reference genotypes for future ancestry investigations in forensic cases. The 33-plex assay also includes pigmentation predictive SNPs, but this study primarily focused on Eurasian population differentiation using 33-plex and its combination with the other two AI-SNP sets.

Evaluation of reliability on STR typing at leukemic patients used for forensic purposes

Over the past decades, main advances in the field of molecular biology, coupled with benefits in genomic technologies, have led to detailed molecular investigations in the genetic diversity generated by researchers. Short tandem repeat (STR) loci are polymorphic loci found throughout all eukaryotic genome. DNA profiling identification, parental testing and kinship analysis by analysis of STR loci have been widely used in forensic sciences since 1993. Malignant tissues may sometimes be the source of biological material for forensic analysis, including identification of individuals or paternity testing. There are a number of studies on microsatellite instability in different types of tumors by comparing the STR profiles of malignant and healthy tissues on the same individuals. Defects in DNA repair pathways (non-repair or mis-repair) and metabolism lead to an accumulation of microsatellite alterations in genomic DNA of various cancer types that result genomic instabilities on forensic analyses. Common forms of genomic instability are loss of heterozygosity (LOH) and microsatellite instability (MSI). In this study, the applicability of autosomal STR markers, which are routinely used in forensic analysis, were investigated in order to detect genotypes in blood samples collected from leukemic patients to estimate the reliability of the results when malignant tissues are used as a source of forensic individual identification. Specimens were collected from 90 acute and 10 chronic leukemia volunteers with oral swabs as well as their paired peripheral blood samples from the Oncology Centre of the Department of Hematology at Istanbul University, during the years 2010–2011. Specimens were tested and compared with 16 somatic STR loci (CSFIPO, THO1, TPOX, vWA, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11 and FGA) widely used in forensic identification and kinship. Only two STR instabilities were encountered among 100 specimens. An MSI in the FGA loci and a LOH in the D2S1338 loci were determined in two individuals separately. Our results demonstrate that the use of the biological samples from leukemia patients in forensic identification and kinship testing is questionable, especially if known microsatellite instability is available. Genetic instabilities may alter the STR polymorphism, leading to potential errors on forensic identification of individuals. Therefore, typing of autosomal STRs from leukemia patients should be performed with both healthy and malignant tissue samples of individual as references.

Demonstration of false inclusion risks of duo parentage analyses in the Turkish population in light of parentage acceptance criteria

In routine parentage tests, trio analyses (father-mother-child) are preferred. Under certain circumstances, laboratories may have to perform duo analysis (without mother/father). However, duo analyses increase the risk of false inclusions. This paper aimed to evaluate the false inclusion risks of duo analyses in the Turkish population from the point of forensic applications and the Turkish judicial system. Children from 400 previously analysed cases were compared separately with fathers and mothers of other cases by using a computer programme. From the total 345,006 comparisons, in 16 comparisons, no Short Tandem Repeat (STR) mismatch was observed at 15 STR loci between the child and an unrelated parent. In other words, duo tests provided a coincidental second mother or father to 16 children. In almost all of these cases, the probabilities of paternity estimation values are greater than Turkish Judicial System’s parentage acceptance limit, which is 99.73%. According to results, we suggested that trio cases should be performed as much as possible and the parentage acceptance limit, which is 99.73%, should be re-evaluated by a law maker’s commission to prevent false inclusion parentage cases in Turkey.

Estimation of the Y-chromosomal short tandem repeat (Y-STR) mutation rates in Turkey

Abstract Background: The Non-recombining region of the Y-chromosome (NRY) is transferred from father to son in an unchanged form without recombination in meiosis. Since Short tandem repeats on Y-chromosome (Y-STRs) in this region do not have any recombination, these regions are identical in all male individuals who are related to the father except for mutations. Therefore, these regions gain importance in identification for the forensic sciences or determination of paternity. In determination of paternity, if mismatches are observed between father and child, population-specific mutation rates should be used to determine whether it is a mutation or a true exclusion. Therefore in this study, we aim to determine the mutation rates of 17 Y-STR loci in Turkey. Material and methods: 17 Y-STR loci were typed by using AmpFlSTR® Yfiler™ Kit in 90 volunteer father-son pairs. Mutation rates were calculated and compared with other populations. Results: The mutations were found between three father-son pairs at DYS439 and DYS458 loci. In addition, a duplication in DYS389 II loci* 30, 31 was observed. The average mutation rate was determined as 1.96×10−3 for Turkish population. Conclusion: This investigation will contribute to minimize the possibility of false exclusion of the father-son and kinship relations.

Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing

Inferring ancestry and physical characteristics of an unknown individual can contribute to the direction of the investigation and to clarify the event for unknown contributors, cold cases or identification of missing persons and disaster victims. The objective of this study is to develop a custom SNP panel on massively parallel sequencing devices for predicting the biogeographic ancestry and phenotype of an individual. We focused on a two‐tier approach to enhance ancestry. Our MPS panel contains two ancestry informative SNP (AISNPs) panels (i.e., Kidd 55 and SWA panel) to differentiate Southwest Asia from Europe and other continental regions. Then we integrated the set of phenotype informative SNPs into a set of AISNPs. The final set of 156 SNPs was evaluated on the following: sensitivity, genotype concordance, mixtures, ancestry assignment, and phenotype prediction. SNP rs6599400 had consistently poor performance and was removed from further analyses. The extreme mixture (1:10) was difficult to interpret for minor contributor. Ancestry assignment and phenotype predictions (for eye, hair and skin) were accurate for samples’ population origin. The results show that the developed panel provides high coverage data that can be used for inferring ancestry and predicting eye, hair, and skin color from the intermediate population regions.

Prediction of human eye colour using highly informative phenotype SNPs (PISNPs)

ABSTRACT One of the rapidly developing areas in human genetics and genomics is detection of candidate Single Nucleotide Polymorphism (SNPs) for human complex traits. These findings can be used in the field of forensics for predicting the externally visible characteristics (EVCs) of a given individual based on a sample of DNA alone. Eye colour is currently the most thoroughly investigated EVC for forensic genetic applications. In this study, eye colour prediction performance of two currently available major methods was assessed in a set of 100 individuals from Turkey by applying the two statistical approaches of multinomial logistic regression (MLR) and Bayes analysis using each statistical approach’s online portal (https://hirisplex.erasmusmc.nl/ and http://mathgene.usc.es/snipper/eyeclassifier.html) designed for SNP-based forensic prediction for this phenotype. On one hand, eye colour prediction results for IrisPlex SNPs have a high success rate for correctly predicting blue/brown phenotypes but not for green-hazel or intermediate dark phenotypes. On the other hand, Snipper analysis improved detection of intermediate phenotypes but increased the number of unclassified individuals given the prediction probability threshold applied. This study adds data that can be used as a reference for future eye colour prediction investigations in forensic cases.

Application of next generation sequencing in forensic science [Yeni nesil dizilemenin adli bilimlerde kullanýmý]

Next Generation Sequencing (NGS) Technology has been emerged and started to use in genetic research since the 2000s. Until today, various methods which are faster, high throughput and low cost have been developed. NGS Technologies have been gradually developed and the quality of sequencing has been reached the high level and forensic genetics labs have moved to this technology for recent years. NGS Technologies provide new opportunities for forensic genetics research. NGS Technologies enable to analysis of many forensic genetic markers (as STRs, SNPs, mRNA) in only one experiment. Besides, NGS technologies are applicable for different practices which are essential in forensic researches. Among these, create of a DNA database, ancestry and phenotype studies, monozygotic twin studies, identification of body fluids and species, forensic microbiology studies can be considered. This review has been written to focus on NGS technologies in forensic genetics applications and to be a reference study for next forensic researchers.

Heteropaternal Superfecundation: A Case Report in Turkey

Superfecundation is the fertilization of two or more ova from the same cycle by sperm from separate acts of sexual intercourse. Heteropaternal superfecundation occurs when two different males father fraternal twins. This article reports a case of paternity identification in twins. The results showed that each twin had come from a different father.